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Goz E, Tuller T. Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions. J Comput Biol 2016; 23:641-50. [PMID: 27347769 DOI: 10.1089/cmb.2016.0052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A large number of studies demonstrated the importance of different HIV RNA structural elements at all stages of the viral life cycle. Nevertheless, the significance of many of these structures is unknown, and plausibly new regions containing RNA structure-mediated regulatory signals remain to be identified. An important characteristic of genomic regions carrying functionally significant secondary structures is their mutational robustness, that is, the extent to which a sequence remains constant in spite of despite mutations in terms of its underlying secondary structure. Structural robustness to mutations is expected to be important in the case of functional RNA structures in viruses with high mutation rate; it may prevent fitness loss due to disruption of possibly functional conformations, pointing to the specific significance of the corresponding genomic region. In the current work, we perform a genome-wide computational analysis to detect signals of a direct evolutionary selection for strong folding and RNA structure-based mutational robustness within HIV coding sequences. We provide evidence that specific regions of HIV structural genes undergo an evolutionary selection for strong folding; in addition, we demonstrate that HIV Rev responsive element seems to undergo a direct evolutionary selection for increased secondary structure robustness to point mutations. We believe that our analysis may enable a better understanding of viral evolutionary dynamics at the RNA structural level and may benefit to practical efforts of engineering antiviral vaccines and novel therapeutic approaches.
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Affiliation(s)
- Eli Goz
- 1 Department of Biomedical Engineering, Tel-Aviv University , Ramat Aviv, Israel .,2 SynVaccine Ltd . Ramat Hachayal, Tel Aviv, Israel
| | - Tamir Tuller
- 1 Department of Biomedical Engineering, Tel-Aviv University , Ramat Aviv, Israel .,2 SynVaccine Ltd . Ramat Hachayal, Tel Aviv, Israel .,3 Sagol School of Neuroscience, Tel-Aviv University , Ramat Aviv, Israel
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52
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Endoplasmic Reticulum: The Favorite Intracellular Niche for Viral Replication and Assembly. Viruses 2016; 8:v8060160. [PMID: 27338443 PMCID: PMC4926180 DOI: 10.3390/v8060160] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) is the largest intracellular organelle. It forms a complex network of continuous sheets and tubules, extending from the nuclear envelope (NE) to the plasma membrane. This network is frequently perturbed by positive-strand RNA viruses utilizing the ER to create membranous replication factories (RFs), where amplification of their genomes occurs. In addition, many enveloped viruses assemble progeny virions in association with ER membranes, and viruses replicating in the nucleus need to overcome the NE barrier, requiring transient changes of the NE morphology. This review first summarizes some key aspects of ER morphology and then focuses on the exploitation of the ER by viruses for the sake of promoting the different steps of their replication cycles.
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Abstract
Long terminal repeat (LTR) retrotransposons constitute significant fractions of many eukaryotic genomes. Two ancient families are Ty1/Copia (Pseudoviridae) and Ty3/Gypsy (Metaviridae). The Ty3/Gypsy family probably gave rise to retroviruses based on the domain order, similarity of sequences, and the envelopes encoded by some members. The Ty3 element of Saccharomyces cerevisiae is one of the most completely characterized elements at the molecular level. Ty3 is induced in mating cells by pheromone stimulation of the mitogen-activated protein kinase pathway as cells accumulate in G1. The two Ty3 open reading frames are translated into Gag3 and Gag3-Pol3 polyprotein precursors. In haploid mating cells Gag3 and Gag3-Pol3 are assembled together with Ty3 genomic RNA into immature virus-like particles in cellular foci containing RNA processing body proteins. Virus-like particle Gag3 is then processed by Ty3 protease into capsid, spacer, and nucleocapsid, and Gag3-Pol3 into those proteins and additionally, protease, reverse transcriptase, and integrase. After haploid cells mate and become diploid, genomic RNA is reverse transcribed into cDNA. Ty3 integration complexes interact with components of the RNA polymerase III transcription complex resulting in Ty3 integration precisely at the transcription start site. Ty3 activation during mating enables proliferation of Ty3 between genomes and has intriguing parallels with metazoan retrotransposon activation in germ cell lineages. Identification of nuclear pore, DNA replication, transcription, and repair host factors that affect retrotransposition has provided insights into how hosts and retrotransposons interact to balance genome stability and plasticity.
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54
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Swann J, Murry J, Young JAT. Cytosolic sulfotransferase 1A1 regulates HIV-1 minus-strand DNA elongation in primary human monocyte-derived macrophages. Virol J 2016; 13:30. [PMID: 26906565 PMCID: PMC4765207 DOI: 10.1186/s12985-016-0491-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/19/2016] [Indexed: 11/23/2022] Open
Abstract
Background The cellular sulfonation pathway modulates key steps of virus replication. This pathway comprises two main families of sulfonate-conjugating enzymes: Golgi sulfotransferases, which sulfonate proteins, glycoproteins, glycolipids and proteoglycans; and cytosolic sulfotransferases (SULTs), which sulfonate various small molecules including hormones, neurotransmitters, and xenobiotics. Sulfonation controls the functions of numerous cellular factors such as those involved in cell-cell interactions, cell signaling, and small molecule detoxification. We previously showed that the cellular sulfonation pathway regulates HIV-1 gene expression and reactivation from latency. Here we show that a specific cellular sulfotransferase can regulate HIV-1 replication in primary human monocyte-derived macrophages (MDMs) by yet another mechanism, namely reverse transcription. Methods MDMs were derived from monocytes isolated from donor peripheral blood mononuclear cells (PBMCs) obtained from the San Diego Blood Bank. After one week in vitro cell culture under macrophage-polarizing conditions, MDMs were transfected with sulfotranserase-specific or control siRNAs and infected with HIV-1 or SIV constructs expressing a luciferase reporter. Infection levels were subsequently monitored by luminescence. Western blotting was used to assay siRNA knockdown and viral protein levels, and qPCR was used to measure viral RNA and DNA products. Results We demonstrate that the cytosolic sulfotransferase SULT1A1 is highly expressed in primary human MDMs, and through siRNA knockdown experiments, we show that this enzyme promotes infection of MDMs by single cycle VSV-G pseudotyped human HIV-1 and simian immunodeficiency virus vectors and by replication-competent HIV-1. Quantitative PCR analysis revealed that SULT1A1 affects HIV-1 replication in MDMs by modulating the kinetics of minus-strand DNA elongation during reverse transcription. Conclusions These studies have identified SULT1A1 as a cellular regulator of HIV-1 reverse transcription in primary human MDMs. The normal substrates of this enzyme are small phenolic-like molecules, raising the possibility that one or more of these substrates may be involved. Targeting SULT1A1 and/or its substrate(s) may offer a novel host-directed strategy to improve HIV-1 therapeutics. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0491-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Justine Swann
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA. .,University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Jeff Murry
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA. .,Gilead Sciences, 333 Lakeside Drive, Foster City, CA, 94401, USA.
| | - John A T Young
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA. .,Roche Innovation Center Basel, F.Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.
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Vargiu L, Rodriguez-Tomé P, Sperber GO, Cadeddu M, Grandi N, Blikstad V, Tramontano E, Blomberg J. Classification and characterization of human endogenous retroviruses; mosaic forms are common. Retrovirology 2016; 13:7. [PMID: 26800882 PMCID: PMC4724089 DOI: 10.1186/s12977-015-0232-y] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/16/2015] [Indexed: 02/06/2023] Open
Abstract
Background Human endogenous retroviruses (HERVs) represent the inheritance of ancient germ-line cell infections by exogenous retroviruses and the subsequent transmission of the integrated proviruses to the descendants. ERVs have the same internal structure as exogenous retroviruses. While no replication-competent HERVs have been recognized, some retain up to three of four intact ORFs. HERVs have been classified before, with varying scope and depth, notably in the RepBase/RepeatMasker system. However, existing classifications are bewildering. There is a need for a systematic, unifying and simple classification. We strived for a classification which is traceable to previous classifications and which encompasses HERV variation within a limited number of clades. Results The human genome assembly GRCh 37/hg19 was analyzed with RetroTector, which primarily detects relatively complete Class I and II proviruses. A total of 3173 HERV sequences were identified. The structure of and relations between these proviruses was resolved through a multi-step classification procedure that involved a novel type of similarity image analysis (“Simage”) which allowed discrimination of heterogeneous (noncanonical) from homogeneous (canonical) HERVs. Of the 3173 HERVs, 1214 were canonical and segregated into 39 canonical clades (groups), belonging to class I (Gamma- and Epsilon-like), II (Beta-like) and III (Spuma-like). The groups were chosen based on (1) sequence (nucleotide and Pol amino acid), similarity, (2) degree of fit to previously published clades, often from RepBase, and (3) taxonomic markers. The groups fell into 11 supergroups. The 1959 noncanonical HERVs contained 31 additional, less well-defined groups. Simage analysis revealed several types of mosaicism, notably recombination and secondary integration. By comparing flanking sequences, LTRs and completeness of gene structure, we deduced that some noncanonical HERVs proliferated after the recombination event. Groups were further divided into envelope subgroups (altogether 94) based on sequence similarity and characteristic “immunosuppressive domain” motifs. Intra and inter(super)group, as well as intraclass, recombination involving envelope genes (“env snatching”) was a common event. LTR divergence indicated that HERV-K(HML2) and HERVFC had the most recent integrations, HERVL and HUERSP3 the oldest. Conclusions A comprehensive HERV classification and characterization approach was undertaken. It should be applicable for classification of all ERVs. Recombination was common among HERV ancestors. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0232-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Vargiu
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy. .,Center for Advanced Studies, Research and Development in Sardinia, CRS4, Pula, Italy. .,Nurideas S.r.l., Cagliari, Italy.
| | - Patricia Rodriguez-Tomé
- Center for Advanced Studies, Research and Development in Sardinia, CRS4, Pula, Italy. .,Nurideas S.r.l., Cagliari, Italy.
| | - Göran O Sperber
- Physiology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden.
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Vidar Blikstad
- Department of Medical Sciences, Uppsala University Hospital, Dag Hammarskjölds Väg 17, Uppsala, 751 85, Sweden.
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University Hospital, Dag Hammarskjölds Väg 17, Uppsala, 751 85, Sweden.
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Ross NL, Sullivan MO. Importin-4 Regulates Gene Delivery by Enhancing Nuclear Retention and Chromatin Deposition by Polyplexes. Mol Pharm 2015; 12:4488-97. [PMID: 26465823 PMCID: PMC4733562 DOI: 10.1021/acs.molpharmaceut.5b00645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For successful gene delivery, plasmid DNA must be able to access the nucleus in order to be transcribed. Numerous studies have shown that gene delivery occurs more readily in dividing cells, which is attributed to increased nuclear access when the nuclear envelope disassembles during mitosis; however, nonviral carriers continue to have low transfection efficiencies and require large quantities of DNA per cell to achieve reasonable gene transfer, even in dividing cells. Therefore, we hypothesized that using histone-derived nuclear localization sequences (NLS)s to target polyplexes might enhance nuclear delivery by facilitating interactions with histone effectors that mediate nuclear partitioning and retention during mitosis. We discovered a novel interaction between polyplexes linked to histone 3 (H3) N-terminal tail peptides and the histone nuclear import protein importin-4, as evidenced by strong spatial colocalization as well as significantly decreased transfection when importin-4 expression was reduced. A fraction of the histone-targeted polyplexes was also found to colocalize with the retrotranslocon of the endoplasmic reticulum, Sec61. Super resolution microscopy demonstrated a high level of polyplex binding to chromatin postmitosis, and there also was a significant decrease in the amount of chromatin binding following importin-4 knockdown. These results provide evidence that natural histone effectors mediate both nuclear entry and deposition on chromatin by histone-targeted polyplexes, and a translocation event from the endoplasmic reticulum into the cytosol may occur before mitosis to enable the polyplexes to interact with these essential cytoplasmic proteins.
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Affiliation(s)
- Nikki L Ross
- Department of Chemical and Biomolecular Engineering, University of Delaware , 150 Academy Street, Newark, Delaware 19716, United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware , 150 Academy Street, Newark, Delaware 19716, United States
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Bin Hamid F, Kim J, Shin CG. Cellular and viral determinants of retroviral nuclear entry. Can J Microbiol 2015; 62:1-15. [PMID: 26553381 DOI: 10.1139/cjm-2015-0350] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Retroviruses must integrate their cDNA into the host genome to generate proviruses. Viral DNA-protein complexes interact with cellular proteins and produce pre-integration complexes, which carry the viral genome and cross the nuclear pore channel to enter the nucleus and integrate viral DNA into host chromosomal DNA. If the reverse transcripts fail to integrate, linear or circular DNA species such as 1- and 2-long terminal repeats are generated. Such complexes encounter numerous cellular proteins in the cytoplasm, which restrict viral infection and protect the nucleus. To overcome host cell defenses, the pathogens have evolved several evasion strategies. Viral proteins often contain nuclear localization signals, allowing entry into the nucleus. Among more than 1000 proteins identified as required for HIV infection by RNA interference screening, karyopherins, cleavage and polyadenylation specific factor 6, and nucleoporins have been predominantly studied. This review discusses current opinions about the synergistic relationship between the viral and cellular factors involved in nuclear import, with focus on the unveiled mysteries of the host-pathogen interaction, and highlights novel approaches to pinpoint therapeutic targets.
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Affiliation(s)
- Faysal Bin Hamid
- Department of Systems Biotechnology, Chung-Ang University, Ansung 456-756, Republic of Korea.,Department of Systems Biotechnology, Chung-Ang University, Ansung 456-756, Republic of Korea
| | - Jinsun Kim
- Department of Systems Biotechnology, Chung-Ang University, Ansung 456-756, Republic of Korea.,Department of Systems Biotechnology, Chung-Ang University, Ansung 456-756, Republic of Korea
| | - Cha-Gyun Shin
- Department of Systems Biotechnology, Chung-Ang University, Ansung 456-756, Republic of Korea.,Department of Systems Biotechnology, Chung-Ang University, Ansung 456-756, Republic of Korea
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Wang W, Wang J, Qu M, Li X, Zhang J, Zhang H, Wu J, Yu B, Wu H, Kong W, Yu X. Viral Restriction Activity of Feline BST2 Is Independent of Its N-Glycosylation and Induction of NF-κB Activation. PLoS One 2015; 10:e0138190. [PMID: 26379128 PMCID: PMC4574558 DOI: 10.1371/journal.pone.0138190] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/26/2015] [Indexed: 11/18/2022] Open
Abstract
BST2 (CD317, tetherin, HM1.24) is an interferon-inducible transmembrane protein which can directly inhibit the release of enveloped virus particles from infected cells, and its anti-viral activity is reported to be related to the specific topological arrangement of its four structural domains. The N-terminal cytoplasmic tail of feline BST2 (fBST2) is characterized by a shorter N-terminal region compared to those of other known homologs. In this study, we investigated the functional impact of modifying the cytoplasmic tail region of fBST2 and its molecular mechanism. The fBST2 protein with the addition of a peptide at the N-terminus retained anti-release activity against human immunodeficiency virus type-1 and pseudovirus based on feline immunodeficiency virus at a weaker level compared with the wild-type fBST2. However, the fBST2 protein with addition of a peptide internally in the ectodomain proximal to the GPI anchor still retained its anti-viral activity well. Notably, the N-glycosylation state and the cell surface level of the N-terminally modified variants were unlike those of the wild-type protein, while no difference was observed in their intracellular localizations. However, in contrast to human BST2, the wild-type fBST2 did not show the ability to activate NF-κB. Consistent with previous reports, our findings showed that adding a peptide in the cytoplasmic tail region of fBST2 may influence its anti-viral activity. The shorter N-terminal cytoplasmic region of fBST2 compared with human BST2 did not apparently affect its anti-viral activity, which is independent of its N-glycosylation and ability to activate NF-κB.
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Affiliation(s)
- Weiran Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
| | - Jiawen Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
- Center for New Medicine Research, Changchun University of Chinese Medicine, Changchun, Jilin Province, People’s Republic of China
| | - Meng Qu
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
| | - Xiaojun Li
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
| | - Jingyao Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
| | - Haihong Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
| | - Jiaxin Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
| | - Hui Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
- * E-mail: (WK); (XHY)
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, Jilin Province, People’s Republic of China
- * E-mail: (WK); (XHY)
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59
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St. Gelais C, Roger J, Wu L. Non-POU Domain-Containing Octamer-Binding Protein Negatively Regulates HIV-1 Infection in CD4(+) T Cells. AIDS Res Hum Retroviruses 2015; 31:806-16. [PMID: 25769457 DOI: 10.1089/aid.2014.0313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
HIV-1 interacts with numerous cellular proteins during viral replication. Identifying such host proteins and characterizing their roles in HIV-1 infection can deepen our understanding of the dynamic interplay between host and pathogen. We previously identified non-POU domain-containing octamer-binding protein (NonO or p54nrb) as one of host factors associated with catalytically active preintegration complexes (PIC) of HIV-1 in infected CD4(+) T cells. NonO is involved in nuclear processes including transcriptional regulation and RNA splicing. Although NonO has been identified as an HIV-1 interactant in several recent studies, its role in HIV-1 replication has not been characterized. We investigated the effect of NonO on the HIV-1 life cycle in CD4(+) T cell lines and primary CD4(+) T cells using single-cycle and replication-competent HIV-1 infection assays. We observed that short hairpin RNA (shRNA)-mediated stable NonO knockdown in a CD4(+) Jurkat T cell line and primary CD4(+) T cells did not affect cell viability or proliferation, but enhanced HIV-1 infection. The enhancement of HIV-1 infection in Jurkat T cells correlated with increased viral reverse transcription and gene expression. Knockdown of NonO expression in Jurkat T cells modestly enhanced HIV-1 gag mRNA expression and Gag protein synthesis, suggesting that viral gene expression and RNA regulation are the predominantly affected events causing enhanced HIV-1 replication in NonO knockdown (KD) cells. Furthermore, overexpression of NonO in Jurkat T cells reduced HIV-1 single-cycle infection by 41% compared to control cells. Our data suggest that NonO negatively regulates HIV-1 infection in CD4(+) T cells, albeit it has modest effects on early and late stages of the viral life cycle, highlighting the importance of host proteins associated with HIV-1 PIC in regulating viral replication.
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Affiliation(s)
- Corine St. Gelais
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
| | - Jonathan Roger
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
| | - Li Wu
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
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60
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Mu X, Fu Y, Zhu Y, Wang X, Xuan Y, Shang H, Goff SP, Gao G. HIV-1 Exploits the Host Factor RuvB-like 2 to Balance Viral Protein Expression. Cell Host Microbe 2015. [PMID: 26211835 DOI: 10.1016/j.chom.2015.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The correct ratio of the HIV-1 structural protein Gag to the envelope protein (Env) is important for maximal virion infectivity. How the virus ensures the production of Gag and Env proteins in an appropriate ratio remains unknown. We report that HIV-1 exploits the host factor RuvB-like 2 (RVB2) to balance relative expression of Gag and Env for efficient production of infectious virions. RVB2 inhibits Gag expression by interacting with both the encoded Matrix (MA) domain of Gag protein and 5' UTR of the translating mRNA and promoting mRNA degradation in a translation-dependent manner. This inhibitory activity of RVB2 is antagonized by Env through competitive interaction with MA, allowing Gag synthesis to proceed when Env levels are adequate for virion assembly. In HIV-1-positive patients, RVB2 levels positively correlate with viral loads and disease progression status. These findings reveal a mechanism by which HIV-1 regulates its protein expression.
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Affiliation(s)
- Xin Mu
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yajing Fu
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, The First Affiliated Hospital, China Medical University, Shenyang 110001, China
| | - Yiping Zhu
- Department of Biochemistry and Molecular Biophysics, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York NY, 10032, USA
| | - Xinlu Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yifang Xuan
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Shang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, The First Affiliated Hospital, China Medical University, Shenyang 110001, China
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York NY, 10032, USA
| | - Guangxia Gao
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data. Sci Rep 2015; 5:11534. [PMID: 26166306 PMCID: PMC4499804 DOI: 10.1038/srep11534] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/07/2015] [Indexed: 11/10/2022] Open
Abstract
Several pathogenic viruses such as hepatitis B and human immunodeficiency viruses may integrate into the host genome. These virus/host integrations are detectable using paired-end next generation sequencing. However, the low number of expected true virus integrations may be difficult to distinguish from the noise of many false positive candidates. Here, we propose a novel filtering approach that increases specificity without compromising sensitivity for virus/host chimera detection. Our detection pipeline termed Vy-PER (Virus integration detection bY Paired End Reads) outperforms existing similar tools in speed and accuracy. We analysed whole genome data from childhood acute lymphoblastic leukemia (ALL), which is characterised by genomic rearrangements and usually associated with radiation exposure. This analysis was motivated by the recently reported virus integrations at genomic rearrangement sites and association with chromosomal instability in liver cancer. However, as expected, our analysis of 20 tumour and matched germline genomes from ALL patients finds no significant evidence for integrations by known viruses. Nevertheless, our method eliminates 12,800 false positives per genome (80× coverage) and only our method detects singleton human-phiX174-chimeras caused by optical errors of the Illumina HiSeq platform. This high accuracy is useful for detecting low virus integration levels as well as non-integrated viruses.
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62
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Lee JH, Oh BK, Choi JW. Development of a HIV-1 Virus Detection System Based on Nanotechnology. SENSORS 2015; 15:9915-27. [PMID: 25923937 PMCID: PMC4481885 DOI: 10.3390/s150509915] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/08/2015] [Accepted: 04/20/2015] [Indexed: 12/27/2022]
Abstract
Development of a sensitive and selective detection system for pathogenic viral agents is essential for medical healthcare from diagnostics to therapeutics. However, conventional detection systems are time consuming, resource-intensive and tedious to perform. Hence, the demand for sensitive and selective detection system for virus are highly increasing. To attain this aim, different aspects and techniques have been applied to develop virus sensor with improved sensitivity and selectivity. Here, among those aspects and techniques, this article reviews HIV virus particle detection systems incorporated with nanotechnology to enhance the sensitivity. This review mainly focused on four different detection system including vertically configured electrical detection based on scanning tunneling microscopy (STM), electrochemical detection based on direct electron transfer in virus, optical detection system based on localized surface plasmon resonance (LSPR) and surface enhanced Raman spectroscopy (SERS) using plasmonic nanoparticle.
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Affiliation(s)
- Jin-Ho Lee
- Department of Chemical & Biomolecular Engineering, Sogang University, #1 Shinsu-Dong, Mapo-Gu, Seoul 121-742, Korea.
| | - Byung-Keun Oh
- Department of Chemical & Biomolecular Engineering, Sogang University, #1 Shinsu-Dong, Mapo-Gu, Seoul 121-742, Korea.
| | - Jeong-Woo Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, #1 Shinsu-Dong, Mapo-Gu, Seoul 121-742, Korea.
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63
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Zeng M, Hu Z, Shi X, Li X, Zhan X, Li XD, Wang J, Choi JH, Wang KW, Purrington T, Tang M, Fina M, DeBerardinis RJ, Moresco EMY, Pedersen G, McInerney GM, Karlsson Hedestam GB, Chen ZJ, Beutler B. MAVS, cGAS, and endogenous retroviruses in T-independent B cell responses. Science 2014; 346:1486-92. [PMID: 25525240 PMCID: PMC4391621 DOI: 10.1126/science.346.6216.1486] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Multivalent molecules with repetitive structures including bacterial capsular polysaccharides and viral capsids elicit antibody responses through B cell receptor (BCR) crosslinking in the absence of T cell help. We report that immunization with these T cell-independent type 2 (TI-2) antigens causes up-regulation of endogenous retrovirus (ERV) RNAs in antigen-specific mouse B cells. These RNAs are detected via a mitochondrial antiviral signaling protein (MAVS)-dependent RNA sensing pathway or reverse-transcribed and detected via the cGAS-cGAMP-STING pathway, triggering a second, sustained wave of signaling that promotes specific immunoglobulin M production. Deficiency of both MAVS and cGAS, or treatment of MAVS-deficient mice with reverse transcriptase inhibitors, dramatically inhibits TI-2 antibody responses. These findings suggest that ERV and two innate sensing pathways that detect them are integral components of the TI-2 B cell signaling apparatus.
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Affiliation(s)
- Ming Zeng
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Zeping Hu
- Department of Pediatrics and Children's Medical Center Research Institute, and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Xiaolei Shi
- Department of Pediatrics and Children's Medical Center Research Institute, and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Xiao-Dong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. Howard Hughes Medical Institute, Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. Howard Hughes Medical Institute, Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Kuan-wen Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Tiana Purrington
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Maggy Fina
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Ralph J DeBerardinis
- Department of Pediatrics and Children's Medical Center Research Institute, and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Gabriel Pedersen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, SE-171 77 Stockholm, Sweden
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, SE-171 77 Stockholm, Sweden
| | - Gunilla B Karlsson Hedestam
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, SE-171 77 Stockholm, Sweden
| | - Zhijian J Chen
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. Howard Hughes Medical Institute, Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA.
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Bandyopadhyay S, Ray S, Mukhopadhyay A, Maulik U. A review of in silico approaches for analysis and prediction of HIV-1-human protein-protein interactions. Brief Bioinform 2014; 16:830-51. [PMID: 25479794 DOI: 10.1093/bib/bbu041] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Indexed: 12/19/2022] Open
Abstract
The computational or in silico approaches for analysing the HIV-1-human protein-protein interaction (PPI) network, predicting different host cellular factors and PPIs and discovering several pathways are gaining popularity in the field of HIV research. Although there exist quite a few studies in this regard, no previous effort has been made to review these works in a comprehensive manner. Here we review the computational approaches that are devoted to the analysis and prediction of HIV-1-human PPIs. We have broadly categorized these studies into two fields: computational analysis of HIV-1-human PPI network and prediction of novel PPIs. We have also presented a comparative assessment of these studies and proposed some methodologies for discussing the implication of their results. We have also reviewed different computational techniques for predicting HIV-1-human PPIs and provided a comparative study of their applicability. We believe that our effort will provide helpful insights to the HIV research community.
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65
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Luo Y, Muesing MA. Mass spectrometry-based proteomic approaches for discovery of HIV-host interactions. Future Virol 2014; 9:979-992. [PMID: 25544858 DOI: 10.2217/fvl.14.86] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A molecular understanding of viral infection requires a multi-disciplinary approach. Mass spectrometry has emerged as an indispensable tool to investigate the complex and dynamic interactions between HIV-1 and its host. It has been employed to study protein associations, changes in protein abundance and post-translational modifications occurring after viral infection. Here, we review and provide examples of mass spectrometry-based proteomic approaches currently used to explore virus-host interaction. Efforts in this area are certain to accelerate the discovery of the unique molecular strategies utilized by the virus to commandeer the cell as well as mechanisms of host defense.
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Affiliation(s)
- Yang Luo
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, 455 First Avenue 7th Floor, New York, NY 10016, USA
| | - Mark A Muesing
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, 455 First Avenue 7th Floor, New York, NY 10016, USA
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66
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Lv M, Wang J, Zhang J, Zhang B, Wang X, Zhu Y, Zuo T, Liu D, Li X, Wu J, Zhang H, Yu B, Wu H, Zhao X, Kong W, Yu X. Epitope tags beside the N-terminal cytoplasmic tail of human BST-2 alter its intracellular trafficking and HIV-1 restriction. PLoS One 2014; 9:e111422. [PMID: 25347789 PMCID: PMC4210262 DOI: 10.1371/journal.pone.0111422] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/25/2014] [Indexed: 12/02/2022] Open
Abstract
BST-2 blocks the particle release of various enveloped viruses including HIV-1, and this antiviral activity is dependent on the topological arrangement of its four structural domains. Several functions of the cytoplasmic tail (CT) of BST-2 have been previously discussed, but the exact role of this domain remains to be clearly defined. In this study, we investigated the impact of truncation and commonly-used tags addition into the CT region of human BST-2 on its intracellular trafficking and signaling as well as its anti-HIV-1 function. The CT-truncated BST-2 exhibited potent inhibition on Vpu-defective HIV-1 and even wild-type HIV-1. However, the N-terminal HA-tagged CT-truncated BST-2 retained little antiviral activity and dramatically differed from its original protein in the cell surface level and intracellular localization. Further, we showed that the replacement of the CT domain with a hydrophobic tag altered BST-2 function possibly by preventing its normal vesicular trafficking. Notably, we demonstrated that a positive charged motif “KRXK” in the conjunctive region between the cytotail and the transmembrane domain which is conserved in primate BST-2 is important for the protein trafficking and the antiviral function. These results suggest that although the CT of BST-2 is not essential for its antiviral activity, the composition of residues in this region may play important roles in its normal trafficking which subsequently affected its function. These observations provide additional implications for the structure-function model of BST-2.
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Affiliation(s)
- Mingyu Lv
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Jiawen Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
- Center for New Medicine Research, Changchun University of Chinese Medicine, Changchun, P.R. China
| | - Jingyao Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Biao Zhang
- School of Pharmaceutical Sciences, Jilin University, Changchun, P.R. China
| | - Xiaodan Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Yingzi Zhu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Tao Zuo
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Donglai Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Xiaojun Li
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Jiaxin Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Haihong Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Hui Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Xinghong Zhao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
- * E-mail: (WK); (XY)
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, P.R. China
- * E-mail: (WK); (XY)
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67
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Zhu J, Davoli T, Perriera JM, Chin CR, Gaiha GD, John SP, Sigiollot FD, Gao G, Xu Q, Qu H, Pertel T, Sims JS, Smith JA, Baker RE, Maranda L, Ng A, Elledge SJ, Brass AL. Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents. Cell Rep 2014; 9:752-66. [PMID: 25373910 PMCID: PMC4926641 DOI: 10.1016/j.celrep.2014.09.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/06/2014] [Accepted: 09/16/2014] [Indexed: 11/17/2022] Open
Abstract
RNAi screens have implicated hundreds of host proteins as HIV-1 dependency factors (HDFs). While informative, these early studies overlap poorly due to false positives and false negatives. To ameliorate these issues, we combined information from the existing HDF screens together with new screens performed with multiple orthologous RNAi reagents (MORR). In addition to being traditionally validated, the MORR screens and the historical HDF screens were quantitatively integrated by the adaptation of an established analysis program, RIGER, for the collective interpretation of each gene’s phenotypic significance. False positives were addressed by the removal of poorly expressed candidates through gene expression filtering, as well as with GESS, which identifies off-target effects. This workflow produced a quantitatively integrated network of genes that modulate HIV-1 replication. We further investigated the roles of GOLGI49, SEC13, and COG in HIV-1 replication. Collectively, the MORR-RIGER method minimized the caveats of RNAi screening and improved our understanding of HIV-1–host cell interactions.
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Affiliation(s)
- Jian Zhu
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Teresa Davoli
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Jill M Perriera
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Christopher R Chin
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Gaurav D Gaiha
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
| | - Sinu P John
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
| | | | - Geng Gao
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Qikai Xu
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Hongjing Qu
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Thomas Pertel
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
| | - Jennifer S Sims
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
| | - Jennifer A Smith
- ICCB-Longwood Screening Facility, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Richard E Baker
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Louise Maranda
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue, North Worcester, MA 01655, USA
| | - Aylwin Ng
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephen J Elledge
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Abraham L Brass
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA.
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68
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Target silencing of components of the conserved oligomeric Golgi complex impairs HIV-1 replication. Virus Res 2014; 192:92-102. [PMID: 25179963 DOI: 10.1016/j.virusres.2014.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 12/23/2022]
Abstract
All viruses require host cell factors to replicate. A large number of host factors have been identified that participate at numerous points of the human immunodeficiency virus 1 (HIV-1) life cycle. Recent evidence supports a role for components of the trans-Golgi network (TGN) in mediating early steps in the HIV-1 life cycle. The conserved oligomeric Golgi (COG) complex is a heteroctamer complex that functions in coat protein complex I (COPI)-mediated intra-Golgi retrograde trafficking and plays an important role in the maintenance of Golgi structure and integrity as well as glycosylation enzyme homeostasis. The targeted silencing of components of lobe B of the COG complex, namely COG5, COG6, COG7 and COG8, inhibited HIV-1 replication. This inhibition of HIV-1 replication preceded late reverse transcription (RT) but did not affect viral fusion. Silencing of the COG interacting protein the t-SNARE syntaxin 5, showed a similar defect in late RT product formation, strengthening the role of the TGN in HIV replication.
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69
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Identification of molecular sub-networks associated with cell survival in a chronically SIVmac-infected human CD4+ T cell line. Virol J 2014; 11:152. [PMID: 25163480 PMCID: PMC4163169 DOI: 10.1186/1743-422x-11-152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 08/15/2014] [Indexed: 12/31/2022] Open
Abstract
Background The deciphering of cellular networks to determine susceptibility to infection by HIV or the related simian immunodeficiency virus (SIV) is a major challenge in infection biology. Results Here, we have compared gene expression profiles of a human CD4+ T cell line at 24 h after infection with a cell line of the same origin permanently releasing SIVmac. A new knowledge-based-network approach (Inter-Chain-Finder, ICF) has been used to identify sub-networks associated with cell survival of a chronically SIV-infected T cell line. Notably, the method can identify not only differentially expressed key hub genes but also non-differentially expressed, critical, ‘hidden’ regulators. Six out of the 13 predicted major hidden key regulators were among the landscape of proteins known to interact with HIV. Several sub-networks were dysregulated upon chronic infection with SIV. Most prominently, factors reported to be engaged in early stages of acute viral infection were affected, e.g. entry, integration and provirus transcription and other cellular responses such as apoptosis and proliferation were modulated. For experimental validation of the gene expression analyses and computational predictions, individual pathways/sub-networks and significantly altered key regulators were investigated further. We showed that the expression of caveolin-1 (Cav-1), the top hub in the affected protein-protein interaction network, was significantly upregulated in chronically SIV-infected CD4+ T cells. Cav-1 is the main determinant of caveolae and a central component of several signal transduction pathways. Furthermore, CD4 downregulation and modulation of the expression of alternate and co-receptors as well as pathways associated with viral integration into the genome were also observed in these cells. Putatively, these modifications interfere with re-infection and the early replication cycle and inhibit cell death provoked by syncytia formation and bystander apoptosis. Conclusions Thus, by using the novel approach for network analysis, ICF, we predict that in the T cell line chronically infected with SIV, cellular processes that are known to be crucial for early phases of HIV/SIV replication are altered and cellular responses that result in cell death are modulated. These modifications presumably contribute to cell survival despite chronic infection. Electronic supplementary material The online version of this article (doi:10.1186/1743-422X-11-152) contains supplementary material, which is available to authorized users.
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Tan BH, Suzuki Y, Takahashi H, Ying PHR, Takahashi C, Han Q, Chin WX, Chao SH, Sawasaki T, Yamamoto N, Suzuki Y. Identification of RFPL3 protein as a novel E3 ubiquitin ligase modulating the integration activity of human immunodeficiency virus, type 1 preintegration complex using a microtiter plate-based assay. J Biol Chem 2014; 289:26368-26382. [PMID: 25107902 DOI: 10.1074/jbc.m114.561662] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Integration, one of the hallmarks of retrovirus replication, is mediated by a nucleoprotein complex called the preintegration complex (PIC), in which viral DNA is associated with many protein components that are required for completion of the early phase of infection. A striking feature of the PIC is its powerful integration activity in vitro. The PICs from a freshly isolated cytoplasmic extract of infected cells are able to insert viral DNA into exogenously added target DNA in vitro. Therefore, a PIC-based in vitro assay is a reliable system for assessing protein factors influencing retroviral integration. In this study, we applied a microtiter plate-based in vitro assay to a screening study using a protein library that was produced by the wheat germ cell-free protein synthesis system. Using a library of human E3 ubiquitin ligases, we identified RFPL3 as a potential stimulator of human immunodeficiency virus, type 1 (HIV-1) PIC integration activity in vitro. This enhancement of PIC activity by RFPL3 was likely to be attributed to its N-terminal RING domain. To further understand the functional role of RFPL3 in HIV infection, we created a human cell line overexpressing RFPL3. Immunoprecipitation analysis revealed that RFPL3 was associated with the human immunodeficiency virus, type 1 PICs in infected cells. More importantly, single-round HIV-1 infection was enhanced significantly by RFPL3 expression. Our proteomic approach displays an advantage in the identification of new cellular proteins affecting the integration activity of the PIC and, therefore, contributes to the understanding of functional interaction between retroviral integration complexes and host factors.
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Affiliation(s)
- Beng Hui Tan
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Yasutsugu Suzuki
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Hirotaka Takahashi
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Pamela Ho Rui Ying
- Veterinary Bioscience, Life Sciences and Chemical Technology, Ngee Ann Polytechnic, 535 Clementi Road, Singapore 599489, Singapore
| | - Chikako Takahashi
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Qi'En Han
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Wei Xin Chin
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Sheng-Hao Chao
- Expression Engineering Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Tatsuya Sawasaki
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan, and
| | - Naoki Yamamoto
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore,.
| | - Youichi Suzuki
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore,; Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.
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71
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Lin YJ, Chen CY, Jeang KT, Liu X, Wang JH, Hung CH, Tsang H, Lin TH, Liao CC, Huang SM, Lin CW, Ho MW, Chien WK, Chen JH, Ho TJ, Tsai FJ. Ring finger protein 39 genetic variants associate with HIV-1 plasma viral loads and its replication in cell culture. Cell Biosci 2014; 4:40. [PMID: 25126410 PMCID: PMC4131809 DOI: 10.1186/2045-3701-4-40] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/29/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The human immunodeficiency virus (HIV-1) exploits host proteins to complete its life cycle. Genome-wide siRNA approaches suggested that host proteins affect HIV-1 replication. However, the results barely overlapped. RING finger protein 39 (RNF39) has been identified from genome-wide association studies. However, its function during HIV-1 replication remains unclear. METHODS AND RESULTS We investigated the relationship between common RNF39 genetic variants and HIV-1 viral loads. The effect of RNF39 protein knockdown or overexpression on HIV-1 replication was then investigated in different cell lines. Two genetic variants were associated with HIV-1 viral loads. Patients with the ht1-GG/GG haplotype presented lower RNF39 expression levels and lower HIV-1 viral load. RNF39 knockdown inhibited HIV-1 expression. CONCLUSIONS RNF39 protein may be involved in HIV-1 replication as observed in genetic studies on patients with HIV-1 and in in vitro cell cultures.
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Affiliation(s)
- Ying-Ju Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Chia-Yen Chen
- Viral Biochemistry Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kuan-Teh Jeang
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Xiang Liu
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jen-Hsien Wang
- Section of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chien-Hui Hung
- Graduate Institute of Clinical Medical Science, Chang-Gung University, Chiayi, Taiwan
| | - Hsinyi Tsang
- The Laboratory of Molecular Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ting-Hsu Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chiu-Chu Liao
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Shao-Mei Huang
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Mao-Wang Ho
- Section of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Wen-Kuei Chien
- Biostatistics Center, China Medical University, Taichung, Taiwan.,Biostatistics Center, Taipei Medical University, Taipei, Taiwan
| | - Jin-Hua Chen
- Biostatistics Center, China Medical University, Taichung, Taiwan.,Biostatistics Center, Taipei Medical University, Taipei, Taiwan
| | - Tsung-Jung Ho
- School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Division of Chinese Medicine, China Medical University Beigang Hospital, Yunlin County, Taiwan.,Division of Chinese Medicine, Tainan Municipal An-Nan Hospital -China Medical University, Tainan, Taiwan
| | - Fuu-Jen Tsai
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Department of Biotechnology, Asia University, Taichung, Taiwan
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72
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The domain landscape of virus-host interactomes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:867235. [PMID: 24991570 PMCID: PMC4065681 DOI: 10.1155/2014/867235] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/19/2014] [Indexed: 12/31/2022]
Abstract
Viral infections result in millions of deaths in the world today. A thorough analysis of virus-host interactomes may reveal insights into viral infection and pathogenic strategies. In this study, we presented a landscape of virus-host interactomes based on protein domain interaction. Compared to the analysis at protein level, this domain-domain interactome provided a unique abstraction of protein-protein interactome. Through comparisons among DNA, RNA, and retrotranscribing viruses, we identified a core of human domains, that viruses used to hijack the cellular machinery and evade the immune system, which might be promising antiviral drug targets. We showed that viruses preferentially interacted with host hub and bottleneck domains, and the degree and betweenness centrality among three categories of viruses are significantly different. Further analysis at functional level highlighted that different viruses perturbed the host cellular molecular network by common and unique strategies. Most importantly, we creatively proposed a viral disease network among viral domains, human domains and the corresponding diseases, which uncovered several unknown virus-disease relationships that needed further verification. Overall, it is expected that the findings will help to deeply understand the viral infection and contribute to the development of antiviral therapy.
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Hasan M, Yan N. Safeguard against DNA sensing: the role of TREX1 in HIV-1 infection and autoimmune diseases. Front Microbiol 2014; 5:193. [PMID: 24817865 PMCID: PMC4012220 DOI: 10.3389/fmicb.2014.00193] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/11/2014] [Indexed: 12/14/2022] Open
Abstract
Innate immune recognition is crucial for host responses against viral infections, including infection by human immunodeficiency virus 1 (HIV-1). Human cells detect such invading pathogens with a collection of pattern recognition receptors that activate the production of antiviral proteins, such as the cytokine interferon-type I, to initiate antiviral responses immediately as well as the adaptive immune response for long-term protection. To establish infection in the host, many viruses have thus evolved strategies for subversion of these mechanisms of innate immunity. For example, acute infection by HIV-1 and other retroviruses have long been thought to be non-immunogenic, signifying suppression of host defenses by these pathogens. Studies in the past few years have begun to uncover a multifaceted scheme of how HIV-1 evades innate immune detection, especially of its DNA, by exploiting host proteins. This review will discuss the host mechanisms of HIV-1 DNA sensing and viral immune evasion, with a particular focus on TREX1, three prime repair exonuclease 1, a host 3′ exonuclease (also known as DNase III).
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Affiliation(s)
- Maroof Hasan
- Department of Internal Medicine, University of Texas Southwestern Medical Center Dallas, TX, USA ; DDepartment of Microbiology, University of Texas Southwestern Medical Center Dallas, TX, USA
| | - Nan Yan
- Department of Internal Medicine, University of Texas Southwestern Medical Center Dallas, TX, USA ; DDepartment of Microbiology, University of Texas Southwestern Medical Center Dallas, TX, USA
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74
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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75
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Meyerson NR, Rowley PA, Swan CH, Le DT, Wilkerson GK, Sawyer SL. Positive selection of primate genes that promote HIV-1 replication. Virology 2014; 454-455:291-8. [PMID: 24725956 DOI: 10.1016/j.virol.2014.02.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 02/19/2014] [Accepted: 02/28/2014] [Indexed: 12/22/2022]
Abstract
Evolutionary analyses have revealed that most host-encoded restriction factors against HIV have experienced virus-driven selection during primate evolution. However, HIV also depends on the function of many human proteins, called host factors, for its replication. It is not clear whether virus-driven selection shapes the evolution of host factor genes to the extent that it is known to shape restriction factor genes. We show that five out of 40 HIV host factor genes (13%) analyzed do bear strong signatures of positive selection. Some of these genes (CD4, NUP153, RANBP2/NUP358) have been characterized with respect to the HIV lifecycle, while others (ANKRD30A/NY-BR-1 and MAP4) remain relatively uncharacterized. One of these, ANKRD30A, shows the most rapid evolution within this set of genes and is induced by interferon stimulation. We discuss how evolutionary analysis can aid the study of host factors for viral replication, just as it has the study of host immunity systems.
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Affiliation(s)
- Nicholas R Meyerson
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA
| | - Paul A Rowley
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA
| | - Christina H Swan
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA; Regents School of Austin, 3230 Travis Country Circle, Austin, TX, USA
| | - Dona T Le
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Sara L Sawyer
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA.
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76
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Schroeder M, Kolodzik A, Pfaff K, Priyadarshini P, Krepstakies M, Hauber J, Rarey M, Meier C. In silico design, synthesis, and screening of novel deoxyhypusine synthase inhibitors targeting HIV-1 replication. ChemMedChem 2014; 9:940-52. [PMID: 24616161 DOI: 10.1002/cmdc.201300481] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/29/2014] [Indexed: 01/26/2023]
Abstract
The human enzyme deoxyhypusine synthase (DHS) is an important host cell factor that participates in the post-translational hypusine modification of eukaryotic initiation factor 5A (eIF-5A). Hypusine-modified eIF-5A plays a role in a number of diseases, including HIV infection/AIDS. Thus, DHS represents a novel and attractive drug target. So far, four crystal structures are available, and various substances have been tested for inhibition of human DHS. Among these inhibitors, N-1-guanyl-1,7-diaminoheptane (GC7) has been co-crystallized in the active site of DHS. However, despite its potency, GC7 is not selective enough to be used in drug applications. Therefore, new compounds that target DHS are needed. Herein we report the in silico design, chemical synthesis, and biological evaluation of new DHS inhibitors. One of these inhibitors showed dose-dependent inhibition of DHS in vitro, as well as suppression of HIV replication in cell cultures. Furthermore, the compound exhibited no cytotoxic effects at active concentrations. Thus, this designed compound demonstrated proof of principle and represents a promising starting point for the development of new drug candidates to specifically interfere with DHS activity.
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Affiliation(s)
- Marcus Schroeder
- Organic Chemistry, Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg (Germany)
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77
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Clemente MI, Álvarez S, Serramía MJ, Martínez-Bonet M, Muñoz-Fernández MÁ. Prostaglandin E2 reduces the release and infectivity of new cell-free virions and cell-to-cell HIV-1 transfer. PLoS One 2014; 9:e85230. [PMID: 24586238 PMCID: PMC3934822 DOI: 10.1371/journal.pone.0085230] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/25/2013] [Indexed: 12/23/2022] Open
Abstract
Background The course of human immunodeficiency virus type-1 (HIV-1) infection is influenced by a complex interplay between viral and host factors. HIV infection stimulates several proinflammatory genes, such as cyclooxigense-2 (COX-2), which leads to an increase in prostaglandin (PG) levels in the plasma of HIV-1-infected patients. These genes play an indeterminate role in HIV replication and pathogenesis. The effect of prostaglandin E2 (PGE2) on HIV infection is quite controversial and even contradictory, so we sought to determine the role of PGE2 and the signal transduction pathways involved in HIV infection to elucidate possible new targets for antiretrovirals. Results Our results suggest that PGE2 post-infection treatment acts in the late stages of the viral cycle to reduce HIV replication. Interestingly, viral protein synthesis was not affected, but a loss of progeny virus production was observed. No modulation of CD4 CXCR4 and CCR5 receptor expression, cell proliferation, or activation after PGE2 treatment was detected. Moreover, PGE2 induced an increase in intracellular cAMP (cyclic AMP) levels through the EP2/EP4 receptors. PGE2 effects were mimicked by dbcAMP and by a specific Epac (exchange protein directly activated by cyclic AMP) agonist, 8-Cpt-cAMP. Treatment with PGE2 increased Rap1 activity, decreased RhoA activity and subsequently reduced the polymerization of actin by approximately 30% compared with untreated cells. In connection with this finding, polarized viral assembly platforms enriched in Gag were disrupted, altering HIV cell-to-cell transfer and the infectivity of new virions. Conclusions Our results demonstrate that PGE2, through Epac and Rap activation, alters the transport of newly synthesized HIV-1 components to the assembly site, reducing the release and infectivity of new cell-free virions and cell-to-cell HIV-1 transfer.
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Affiliation(s)
- María Isabel Clemente
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Zaragoza, Spain
| | - Susana Álvarez
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Zaragoza, Spain
| | - María Jesús Serramía
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Zaragoza, Spain
| | - Marta Martínez-Bonet
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Zaragoza, Spain
| | - María Ángeles Muñoz-Fernández
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Zaragoza, Spain
- * E-mail:
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78
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Understanding HIV-1 protease autoprocessing for novel therapeutic development. Future Med Chem 2014; 5:1215-29. [PMID: 23859204 DOI: 10.4155/fmc.13.89] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the infected cell, HIV-1 protease (PR) is initially synthesized as part of the GagPol polyprotein. PR autoprocessing is a virus-specific process by which the PR domain embedded in the precursor catalyzes proteolytic reactions responsible for liberation of free mature PRs, which then recognize and cleave at least ten different peptide sequences in the Gag and GagPol polyproteins. Despite extensive structure and function studies of the mature PRs as well as the successful development of ten US FDA-approved catalytic-site inhibitors, the precursor autoprocessing mechanism remains an intriguing yet-to-be-solved puzzle. This article discusses current understanding of the autoprocessing mechanism, in an effort to prompt the development of novel anti-HIV drugs that selectively target precursor autoprocessing.
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79
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Abstract
HIV integrase (IN) catalyzes the insertion into the genome of the infected human cell of viral DNA produced by the retrotranscription process. The discovery of raltegravir validated the existence of the IN, which is a new target in the field of anti-HIV drug research. The mechanism of catalysis of IN is depicted, and the characteristics of the inhibitors of the catalytic site of this viral enzyme are reported. The role played by the resistance is elucidated, as well as the possibility of bypassing this problem. New approaches to block the integration process are depicted as future perspectives, such as development of allosteric IN inhibitors, dual inhibitors targeting both IN and other enzymes, inhibitors of enzymes that activate IN, activators of IN activity, as well as a gene therapy approach.
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Affiliation(s)
- Roberto Di Santo
- Dipartimento
di Chimica e
Tecnologie del Farmaco, Istituto Pasteur, Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, P.le Aldo Moro 5, I-00185 Rome, Italy
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80
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Marno KM, Ogunkolade BW, Pade C, Oliveira NMM, O'Sullivan E, McKnight Á. Novel restriction factor RNA-associated early-stage anti-viral factor (REAF) inhibits human and simian immunodeficiency viruses. Retrovirology 2014; 11:3. [PMID: 24410916 PMCID: PMC3895926 DOI: 10.1186/1742-4690-11-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 11/28/2013] [Indexed: 01/09/2023] Open
Abstract
Background The discovery of novel anti-viral restriction factors illuminates unknown aspects of innate sensing and immunity. We identified RNA-associated Early-stage Anti-viral Factor (REAF) using a whole genome siRNA screen for restriction factors to human immunodeficiency virus (HIV) that act in the early phase of viral replication. Results We observed more than 50 fold rescue of HIV-1 infection, using a focus forming unit (FFU) assay, following knockdown of REAF by specific siRNA. Quantitative PCR was used to show that REAF knockdown results in an increase of early and late reverse transcripts which impacts the level of integration. REAF thus appears to act at an early stage of the viral life cycle during reverse transcription. Conversely when REAF is over-expressed in target cells less infected cells are detectable and fewer reverse transcripts are produced. Human REAF can also inhibit HIV-2 and simian immunodeficiency virus (SIV) infection. REAF associates with viral nucleic acids and may act to prevent reverse transcription. Conclusions This report firmly places REAF alongside APOBECs and SAMHD1 as a potent inhibitor of HIV replication acting early in the replication cycle, just after cell entry. We propose that REAF is part of an anti-viral surveillance system destroying incoming retroviruses. This novel mechanism could apply to invasion of cells by any intracellular pathogen.
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Affiliation(s)
| | | | | | | | | | - Áine McKnight
- Centre for Immunology and Infectious Disease, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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81
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Henning MS, Dubose BN, Burse MJ, Aiken C, Yamashita M. In vivo functions of CPSF6 for HIV-1 as revealed by HIV-1 capsid evolution in HLA-B27-positive subjects. PLoS Pathog 2014; 10:e1003868. [PMID: 24415937 PMCID: PMC3887095 DOI: 10.1371/journal.ppat.1003868] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 11/22/2013] [Indexed: 11/21/2022] Open
Abstract
The host protein CPSF6 possesses a domain that can interact with the HIV-1 capsid (CA) protein. CPSF6 has been implicated in regulating HIV-1 nuclear entry. However, its functional significance for HIV-1 replication has yet to be firmly established. Here we provide evidence for two divergent functions of CPSF6 for HIV-1 replication in vivo. We demonstrate that endogenous CPSF6 exerts an inhibitory effect on naturally occurring HIV-1 variants in individuals carrying the HLA-B27 allele. Conversely, we find a strong selective pressure in these individuals to preserve CPSF6 binding, while escaping from the restrictive activity by CPSF6. This active maintenance of CPSF6 binding during HIV-1 CA evolution in vivo contrasts with the in vitro viral evolution, which can reduce CPSF6 binding to evade from CPSF6-mediated restriction. Thus, these observations argue for a beneficial role of CPSF6 for HIV-1 in vivo. CPSF6-mediated restriction renders HIV-1 less dependent or independent from TNPO3, RanBP2 and Nup153, host factors implicated in HIV-1 nuclear entry. However, viral evolution that maintains CPSF6 binding in HLA-B27+ subjects invariably restores the ability to utilize these host factors, which may be the major selective pressure for CPSF6 binding in vivo. Our study uncovers two opposing CA-dependent functions of CPSF6 in HIV-1 replication in vivo; however, the benefit for binding CPSF6 appears to outweigh the cost, providing support for a vital function of CPSF6 during HIV-1 replication in vivo. The viral capsid (CA) protein of HIV-1 determines both the ability to infect non-dividing cells and the utilization of host factors implicated in nuclear entry. Understanding how CA controls these two properties is critical. CPSF6, a CA-interacting host protein, may be important for these properties but its precise role remains unclear. Here we provide direct evidence for the involvement of endogenous CPSF6 during HIV-1 infection. We found that CPSF6 blocks CA mutants that are impaired for infection of non-dividing cells. This CPSF6-mediated inhibition also targets early escape variants that arise in HIV-1 infected HLA-B27+ patients. Moreover, this CPSF6-mediated inhibition, together with robust CTL response, appears to be critical for viral suppression, because viruses derived after late viral breakthrough in these individuals were no longer sensitive to the antiviral activity of CPSF6. However, we also report indirect evidence for a potentially beneficial role for CPSF6 in HIV-1 replication, because escape from this inhibition in vivo was paradoxically accompanied by a strict preservation of the CPSF6 binding pocket. These results highlight the unique characteristics of the HIV-CPSF6 interactions in which CPSF6 can be either beneficial or detrimental for viral replication in a CA-specific manner.
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Affiliation(s)
- Matthew S. Henning
- Aaron Diamond AIDS Research Center, New York, New York, United States of America
| | - Brittany N. Dubose
- Aaron Diamond AIDS Research Center, New York, New York, United States of America
| | - Mallori J. Burse
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Masahiro Yamashita
- Aaron Diamond AIDS Research Center, New York, New York, United States of America
- * E-mail:
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82
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Rajsbaum R, García-Sastre A, Versteeg GA. TRIMmunity: the roles of the TRIM E3-ubiquitin ligase family in innate antiviral immunity. J Mol Biol 2013; 426:1265-84. [PMID: 24333484 DOI: 10.1016/j.jmb.2013.12.005] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 12/24/2022]
Abstract
Tripartite motif (TRIM) proteins have been implicated in multiple cellular functions, including antiviral activity. Research efforts so far indicate that the antiviral activity of TRIMs relies, for the most part, on their function as E3-ubiquitin ligases. A substantial number of the TRIM family members have been demonstrated to mediate innate immune cell signal transduction and subsequent cytokine induction. In addition, a subset of TRIMs has been shown to restrict viral replication by directly targeting viral proteins. Although the body of work on the cellular roles of TRIM E3-ubiquitin ligases has rapidly grown over the last years, many aspects of their molecular workings and multi-functionality remain unclear. The antiviral function of many TRIMs seems to be conferred by specific isoforms, by sub-cellular localization and in cell-type-specific contexts. Here we review recent findings on TRIM antiviral functions, current limitations and an outlook for future research.
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Affiliation(s)
- Ricardo Rajsbaum
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Gijs A Versteeg
- Max F. Perutz Laboratories, University of Vienna, Doktor-Bohr-Gasse 9/4, 1030 Vienna, Austria
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83
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Abstract
Trim 5α was the first member of the tripartite motif (TRIM) family of proteins that was identified to potently restrict human immunodeficiency virus type 1 (HIV-1) replication. The breadth of antiretroviral activity of TRIM family members is an active area of investigation. In this study, we demonstrate that human Trim 37 possesses anti-HIV-1 activity. This antiretroviral activity and the manner in which it was displayed were implicated by (1) decreased viral replication upon Trim 37 transient overexpression in virus-producing cells, (2) correlation of the reduction of viral infectivity with Trim 37 virion incorporation, (3) increased HIV-1 replication during siRNA depletion of Trim 37 expression, and (4) reduction in viral DNA synthesis upon Trim 37 transient overexpression. Our findings provide the first demonstration, to our knowledge, of the potent antiviral activity of human Trim 37, and implicate an antiviral mechanism whereby Trim 37 interferes with viral DNA synthesis.
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Affiliation(s)
- Azah A Tabah
- MinnCResT Program, Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455; USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455; USA
| | - Keith Tardif
- Myriad Pharmaceuticals, Salt Lake City, UT 84108, USA
| | - Louis M Mansky
- Department of Microbiology, University of Minnesota, Minneapolis, MN 55455; USA.,MinnCResT Program, Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455; USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455; USA
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84
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Highly sensitive localized surface plasmon resonance immunosensor for label-free detection of HIV-1. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2013; 9:1018-26. [DOI: 10.1016/j.nano.2013.03.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 01/28/2023]
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85
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Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Res 2013; 23:2042-52. [PMID: 24026178 PMCID: PMC3847774 DOI: 10.1101/gr.154625.113] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In primates and other animals, reverse transcription of mRNA followed by genomic integration creates retroduplications. Expressed retroduplications are either “retrogenes” coding for functioning proteins, or expressed “processed pseudogenes,” which can function as noncoding RNAs. To date, little is known about the variation in retroduplications in terms of their presence or absence across individuals in the human population. We have developed new methodologies that allow us to identify “novel” retroduplications (i.e., those not present in the reference genome), to find their insertion points, and to genotype them. Using these methods, we catalogued and analyzed 174 retroduplication variants in almost one thousand humans, which were sequenced as part of Phase 1 of The 1000 Genomes Project Consortium. The accuracy of our data set was corroborated by (1) multiple lines of sequencing evidence for retroduplication (e.g., depth of coverage in exons vs. introns), (2) experimental validation, and (3) the fact that we can reconstruct a correct phylogenetic tree of human subpopulations based solely on retroduplications. We also show that parent genes of retroduplication variants tend to be expressed at the M-to-G1 transition in the cell cycle and that M-to-G1 expressed genes have more copies of fixed retroduplications than genes expressed at other times. These findings suggest that cell division is coupled to retrotransposition and, perhaps, is even a requirement for it.
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86
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Lv M, Zhu Y, Wang J, Zhang H, Wang X, Zuo T, Liu D, Zhang J, Wu J, Kong W, Yu X. Purification of eukaryotic tetherin/Vpu proteins and detection of their interaction by ELISA. Protein Expr Purif 2013; 91:112-8. [PMID: 23916489 DOI: 10.1016/j.pep.2013.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/25/2013] [Accepted: 07/27/2013] [Indexed: 10/26/2022]
Abstract
Tetherin/BST-2/CD317 inhibits HIV-1 release from infected cells, while HIV-1 Vpu efficiently antagonizes tetherin based on intermolecular interactions between the transmembrane domains of each protein. In this study, we successfully partially purified His-tagged tetherin with a glycophosphatidylinositol deletion (delGPI) and His-tagged full-length Vpu from transiently transfected 293T cells using affinity chromatography. The in vitro interaction between these purified proteins was observed by a pull-down assay and ELISA. Detection of the Vpu/tetherin interaction by ELISA is a novel approach that would be advantageous for inhibitor screening in vitro. Successful co-purification of the tetherin/Vpu complex also provides a basis for further structural studies.
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Affiliation(s)
- Mingyu Lv
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, People's Republic of China
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87
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Piersanti S, Astrologo L, Licursi V, Costa R, Roncaglia E, Gennetier A, Ibanes S, Chillon M, Negri R, Tagliafico E, Kremer EJ, Saggio I. Differentiated neuroprogenitor cells incubated with human or canine adenovirus, or lentiviral vectors have distinct transcriptome profiles. PLoS One 2013; 8:e69808. [PMID: 23922808 PMCID: PMC3724896 DOI: 10.1371/journal.pone.0069808] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/13/2013] [Indexed: 12/13/2022] Open
Abstract
Several studies have demonstrated the potential for vector-mediated gene transfer to the brain. Helper-dependent (HD) human (HAd) and canine (CAV-2) adenovirus, and VSV-G-pseudotyped self-inactivating HIV-1 vectors (LV) effectively transduce human brain cells and their toxicity has been partly analysed. However, their effect on the brain homeostasis is far from fully defined, especially because of the complexity of the central nervous system (CNS). With the goal of dissecting the toxicogenomic signatures of the three vectors for human neurons, we transduced a bona fide human neuronal system with HD-HAd, HD-CAV-2 and LV. We analysed the transcriptional response of more than 47,000 transcripts using gene chips. Chip data showed that HD-CAV-2 and LV vectors activated the innate arm of the immune response, including Toll-like receptors and hyaluronan circuits. LV vector also induced an IFN response. Moreover, HD-CAV-2 and LV vectors affected DNA damage pathways--but in opposite directions--suggesting a differential response of the p53 and ATM pathways to the vector genomes. As a general response to the vectors, human neurons activated pro-survival genes and neuron morphogenesis, presumably with the goal of re-establishing homeostasis. These data are complementary to in vivo studies on brain vector toxicity and allow a better understanding of the impact of viral vectors on human neurons, and mechanistic approaches to improve the therapeutic impact of brain-directed gene transfer.
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Affiliation(s)
- Stefania Piersanti
- Dipartimento di Biologia e Biotecnologie “Chrales Darwin”, Sapienza, Università di Roma, Roma, Italy
| | - Letizia Astrologo
- Dipartimento di Biologia e Biotecnologie “Chrales Darwin”, Sapienza, Università di Roma, Roma, Italy
| | - Valerio Licursi
- Dipartimento di Biologia e Biotecnologie “Chrales Darwin”, Sapienza, Università di Roma, Roma, Italy
| | - Rossella Costa
- Dipartimento di Biologia e Biotecnologie “Chrales Darwin”, Sapienza, Università di Roma, Roma, Italy
| | - Enrica Roncaglia
- Dipartimento di Scienze Biomediche, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Aurelie Gennetier
- Institut de Génétique Moléculaire de Montpellier, University Montpellier I & II, Montpellier, France
| | - Sandy Ibanes
- Institut de Génétique Moléculaire de Montpellier, University Montpellier I & II, Montpellier, France
| | - Miguel Chillon
- Istituto Pasteur Fondazione Cenci Bolognetti, Roma, Italy
| | - Rodolfo Negri
- Dipartimento di Biologia e Biotecnologie “Chrales Darwin”, Sapienza, Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Roma, Italy
| | - Enrico Tagliafico
- Dipartimento di Scienze Biomediche, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Eric J. Kremer
- Institut de Génétique Moléculaire de Montpellier, University Montpellier I & II, Montpellier, France
| | - Isabella Saggio
- Dipartimento di Biologia e Biotecnologie “Chrales Darwin”, Sapienza, Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Roma, Italy
- Istituto di Biologia e Patologia Molecolari del CNR, Roma, Italy
- * E-mail:
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88
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Abstract
Replication of HIV-1 and other retroviruses is dependent on numerous host proteins in the cells. Some of the host proteins, however, function as restriction factors to block retroviral infection of target cells. The host protein SAMHD1 has been identified as the first mammalian deoxynucleoside triphosphate triphosphohydrolase (dNTPase), which blocks the infection of HIV-1 and other retroviruses in non-cycling immune cells. SAMHD1 protein is highly expressed in human myeloid-lineage cells and CD4+ T-lymphocytes, but its retroviral restriction function is only observed in noncycling cells. Recent studies have revealed biochemical mechanisms of SAMHD1-mediated retroviral restriction. In this review, the latest progress on SAMHD1 research is summarized and the mechanisms by which SAMHD1 mediates retroviral restriction are analyzed. Although the physiological function of SAMHD1 is largely unknown, this review provides perspectives about the role of endogenous SAMHD1 protein in maintaining normal cellular function, such as nucleic acid metabolism and the proliferation of cells.
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89
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Lin YJ, Lan YC, Hung CH, Lin TH, Huang SM, Liao CC, Lin CW, Lai CH, Tien N, Liu X, Ho MW, Chien WK, Chen JH, Wang JH, Tsai FJ. Variants in ZNRD1 gene predict HIV-1/AIDS disease progression in a Han Chinese population in Taiwan. PLoS One 2013; 8:e67572. [PMID: 23874430 PMCID: PMC3706582 DOI: 10.1371/journal.pone.0067572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/20/2013] [Indexed: 12/30/2022] Open
Abstract
Patients demonstrate notable variations in disease progression following human immunodeficiency virus (HIV) infection. We aimed to identify ZNRD1 and RNF39 genetic variants linked to AIDS progression. We conducted a genetic association study in HIV-1-infected Han Chinese patients residing in Taiwan. The clinical characteristics of 143 HIV-1-infected patients were measured, and patients were split into 2 groups: AIDS progression and AIDS non-progression. Genotyping of ZNRD1 and RNF39 was performed in all participants. We found that patients in the AIDS progression group had higher HIV-1 viral loads and lower CD4 cell counts than did patients in the AIDS non-progression group. The frequency of the AA genotype of ZNRD1 (rs16896970) was lower in the AIDS progression group than in the AIDS non-progression group. Patients with AA genotypes had lower levels of HIV-1 viral loads and higher levels of CD4 cell counts than did patients with AG+GG genotypes. AIDS progression in patients with the AA group is significantly different from that in patients with the AG and GG groups by using Kaplan-Meier survival analysis. The hazard ratio for progression was lower in the AA group than in the AG and GG groups. We identified a SNP that contributes to AIDS progression in HIV-1-infected patients in this population. This SNP had a significant protective influence on AIDS progression, and polymorphisms of the ZNRD1 gene may play a role in the pathogenesis of HIV-1 infection.
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Affiliation(s)
- Ying-Ju Lin
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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90
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Bohl CR, Abrahamyan LG, Wood C. Human Ubc9 is involved in intracellular HIV-1 Env stability after trafficking out of the trans-Golgi network in a Gag dependent manner. PLoS One 2013; 8:e69359. [PMID: 23861967 PMCID: PMC3704627 DOI: 10.1371/journal.pone.0069359] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/07/2013] [Indexed: 01/03/2023] Open
Abstract
The cellular E2 Sumo conjugase, Ubc9 interacts with HIV-1 Gag, and is important for the assembly of infectious HIV-1 virions. In the previous study we demonstrated that in the absence of Ubc9, a defect in virion assembly was associated with decreased levels of mature intracellular Envelope (Env) that affected Env incorporation into virions and virion infectivity. We have further characterized the effect of Ubc9 knockdown on HIV Env processing and assembly. We found that gp160 stability in the endoplasmic reticulum (ER) and its trafficking to the trans-Golgi network (TGN) were unaffected, indicating that the decreased intracellular mature Env levels in Ubc9-depleted cells were due to a selective degradation of mature Env gp120 after cleavage from gp160 and trafficked out of the TGN. Decreased levels of Gag and mature Env were found to be associated with the plasma membrane and lipid rafts, which suggest that these viral proteins were not trafficked correctly to the assembly site. Intracellular gp120 were partially rescued when treated with a combination of lysosome inhibitors. Taken together our results suggest that in the absence of Ubc9, gp120 is preferentially degraded in the lysosomes likely before trafficking to assembly sites leading to the production of defective virions. This study provides further insight in the processing and packaging of the HIV-1 gp120 into mature HIV-1 virions.
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Affiliation(s)
- Christopher R. Bohl
- Nebraska Center for Virology and the School of Biological Sciences, University of Nebraska, Lincoln, Lincoln, Nebraska, United States of America
| | - Levon G. Abrahamyan
- Nebraska Center for Virology and the School of Biological Sciences, University of Nebraska, Lincoln, Lincoln, Nebraska, United States of America
| | - Charles Wood
- Nebraska Center for Virology and the School of Biological Sciences, University of Nebraska, Lincoln, Lincoln, Nebraska, United States of America
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91
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Monette A, Valiente-Echeverría F, Rivero M, Cohen ÉA, Lopez-Lastra M, Mouland AJ. Dual mechanisms of translation initiation of the full-length HIV-1 mRNA contribute to gag synthesis. PLoS One 2013; 8:e68108. [PMID: 23861855 PMCID: PMC3702555 DOI: 10.1371/journal.pone.0068108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/25/2013] [Indexed: 01/01/2023] Open
Abstract
The precursor group-specific antigen (pr55Gag) is central to HIV-1 assembly. Its expression alone is sufficient to assemble into virus-like particles. It also selects the genomic RNA for encapsidation and is involved in several important virus-host interactions for viral assembly and restriction, making its synthesis essential for aspects of viral replication. Here, we show that the initiation of translation of the HIV-1 genomic RNA is mediated through both a cap-dependent and an internal ribosome entry site (IRES)-mediated mechanisms. In support of this notion, pr55Gag synthesis was maintained at 70% when cap-dependent translation initiation was blocked by the expression of eIF4G- and PABP targeting viral proteases in two in vitro systems and in HIV-1-expressing cells directly infected with poliovirus. While our data reveal that IRES-dependent translation of the viral genomic RNA ensures pr55Gag expression, the synthesis of other HIV-1 proteins, including that of pr160Gag/Pol, Vpr and Tat is suppressed early during progressive poliovirus infection. The data presented herein implies that the unspliced HIV-1 genomic RNA utilizes both cap-dependent and IRES-dependent translation initiation to supply pr55Gag for virus assembly and production.
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MESH Headings
- Cell Line
- Gene Expression Regulation, Viral
- Gene Order
- Genetic Vectors/genetics
- Genome, Viral
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- Peptide Chain Initiation, Translational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Regulatory Sequences, Ribonucleic Acid
- gag Gene Products, Human Immunodeficiency Virus/biosynthesis
- tat Gene Products, Human Immunodeficiency Virus/genetics
- tat Gene Products, Human Immunodeficiency Virus/metabolism
- vpr Gene Products, Human Immunodeficiency Virus/genetics
- vpr Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Anne Monette
- HIV-1 Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Québec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Fernando Valiente-Echeverría
- HIV-1 Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Québec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Matias Rivero
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Éric A. Cohen
- Laboratory of Human Retrovirology, Institut de recherches cliniques de Montréal, Montréal, Quebec, Canada
| | - Marcelo Lopez-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail: (MLL); (AJM)
| | - Andrew J. Mouland
- HIV-1 Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Québec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- * E-mail: (MLL); (AJM)
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92
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A carboxy-terminally truncated human CPSF6 lacking residues encoded by exon 6 inhibits HIV-1 cDNA synthesis and promotes capsid disassembly. J Virol 2013; 87:7726-36. [PMID: 23658440 DOI: 10.1128/jvi.00124-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Since HIV-1 replication is modulated at multiple stages by host cell factors, identification and characterization of those host cell factors are expected to contribute to the development of novel anti-HIV therapeutics. Previous studies showed that a C-terminally truncated cytosolic form of cleavage and polyadenylation-specific factor 6 (CPSF6-358) inhibits HIV-1 infection through interference with HIV-1 trafficking to the nucleus. Here we identified and characterized a different configuration of C-terminally truncated human CPSF6 (hCPSF6-375) through cDNA expression cloning coupled with ganciclovir-mediated lethal selection. Notably, hCPSF6-375, but not mouse CPSF6-358 (mCPSF6-358) as previously reported, remarkably interfered with viral cDNA synthesis after HIV-1 infection. Moreover, we found that hCPSF6-375 aberrantly accelerated the disassembly of the viral capsid in target cells, while CPSF6-358 did not. Sequence comparison of CPSF6-375 and CPSF6-358 cDNAs showed a lack of exon 6 and additional coding sequence for 54 amino acid residues in the C terminus of hCPSF6-375. Mutational analyses revealed that the residues encoded by exon 6, but not the C-terminal 54 residues in hCPSF6-375, is responsible for impaired viral cDNA synthesis by hCPSF6-375. This is the first report demonstrating a novel mode of HIV-1 inhibition by truncated forms of CPSF6 that involves rapid capsid disassembly and inhibition of viral cDNA synthesis. These findings could facilitate an increased understanding of viral cDNA synthesis in light of the viral capsid disassembly.
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93
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Hütter S, Zurnic I, Lindemann D. Foamy virus budding and release. Viruses 2013; 5:1075-98. [PMID: 23575110 PMCID: PMC3705266 DOI: 10.3390/v5041075] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/25/2013] [Accepted: 03/29/2013] [Indexed: 12/21/2022] Open
Abstract
Like all other viruses, a successful egress of functional particles from infected cells is a prerequisite for foamy virus (FV) spread within the host. The budding process of FVs involves steps, which are shared by other retroviruses, such as interaction of the capsid protein with components of cellular vacuolar protein sorting (Vps) machinery via late domains identified in some FV capsid proteins. Additionally, there are features of the FV budding strategy quite unique to the spumaretroviruses. This includes secretion of non-infectious subviral particles and a strict dependence on capsid-glycoprotein interaction for release of infectious virions from the cells. Virus-like particle release is not possible since FV capsid proteins lack a membrane-targeting signal. It is noteworthy that in experimental systems, the important capsid-glycoprotein interaction could be bypassed by fusing heterologous membrane-targeting signals to the capsid protein, thus enabling glycoprotein-independent egress. Aside from that, other systems have been developed to enable envelopment of FV capsids by heterologous Env proteins. In this review article, we will summarize the current knowledge on FV budding, the viral components and their domains involved as well as alternative and artificial ways to promote budding of FV particle structures, a feature important for alteration of target tissue tropism of FV-based gene transfer systems.
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Affiliation(s)
- Sylvia Hütter
- Institute of Virology, Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Fetscherstr. 74, Dresden 01307, Germany; E-Mails: (S.H); (I.Z.)
- DFG-Center for Regenerative Therapies Dresden (CRTD)—Cluster of Excellence, Technische Universität Dresden, Fetscherstr. 105, Dresden 01307, Germany
| | - Irena Zurnic
- Institute of Virology, Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Fetscherstr. 74, Dresden 01307, Germany; E-Mails: (S.H); (I.Z.)
- DFG-Center for Regenerative Therapies Dresden (CRTD)—Cluster of Excellence, Technische Universität Dresden, Fetscherstr. 105, Dresden 01307, Germany
| | - Dirk Lindemann
- Institute of Virology, Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Fetscherstr. 74, Dresden 01307, Germany; E-Mails: (S.H); (I.Z.)
- DFG-Center for Regenerative Therapies Dresden (CRTD)—Cluster of Excellence, Technische Universität Dresden, Fetscherstr. 105, Dresden 01307, Germany
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-351458-6210; Fax: +49-351-458-6310
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94
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Characteristics of the cellular receptor influence the intracellular fate and efficiency of virus infection. J Virol 2013; 87:5916-25. [PMID: 23514894 DOI: 10.1128/jvi.00398-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The intracellular fate of internalized virus-receptor complexes is suspected of influencing the efficiency of virus infection. However, direct evidence of a link between infection and the fate of internalized virus has been difficult to obtain. To directly address this question, we generated human 293 cell lines stably expressing comparable cell surface levels of three different members of the somatostatin receptor family (SSTR) which have natural differences in intracellular trafficking. Utilizing a glycoprotein that recognizes SSTR, we found that distinctive receptor subtype-specific destinations correlated with observable differences in the level of infection. Infection via SSTR-2 and -3 is restricted at a point after receptor binding and endocytosis but prior to penetration into the host cytoplasm. In contrast, entry via SSTR-5 featured a slower internalization with greater dependence on cholesterol. Quantitative real-time PCR showed that virus bound to SSTR-5 was directed to an intracellular environment that allowed near-wild-type (WT) levels of penetration, possibly due to a more favorable complement of host cell proteases, whereas SSTR-2 and -3 directed virions to a degradative compartment in which cytosol penetration was less efficient. Taken together, the results support that the superior receptor capacity of SSTR-5 results from its internalization into a cellular compartment that is more favorable to the cytoplasmic penetration of viral cores and reverse transcription. They suggest that the intracellular destination of internalized complexes is an important characteristic of a virus receptor and may have exerted a selective pressure on the choice of an entry receptor during evolution of viral glycoproteins.
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95
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Dai L, Lidie KB, Chen Q, Adelsberger JW, Zheng X, Huang D, Yang J, Lempicki RA, Rehman T, Dewar RL, Wang Y, Hornung RL, Canizales KA, Lockett SJ, Lane HC, Imamichi T. IL-27 inhibits HIV-1 infection in human macrophages by down-regulating host factor SPTBN1 during monocyte to macrophage differentiation. J Exp Med 2013; 210:517-34. [PMID: 23460728 PMCID: PMC3600911 DOI: 10.1084/jem.20120572] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 01/31/2013] [Indexed: 02/06/2023] Open
Abstract
The susceptibility of macrophages to HIV-1 infection is modulated during monocyte differentiation. IL-27 is an anti-HIV cytokine that also modulates monocyte activation. In this study, we present new evidence that IL-27 promotes monocyte differentiation into macrophages that are nonpermissive for HIV-1 infection. Although IL-27 treatment does not affect expression of macrophage differentiation markers or macrophage biological functions, it confers HIV resistance by down-regulating spectrin β nonerythrocyte 1 (SPTBN1), a required host factor for HIV-1 infection. IL-27 down-regulates SPTBN1 through a TAK-1-mediated MAPK signaling pathway. Knockdown of SPTBN1 strongly inhibits HIV-1 infection of macrophages; conversely, overexpression of SPTBN1 markedly increases HIV susceptibility of IL-27-treated macrophages. Moreover, we demonstrate that SPTBN1 associates with HIV-1 gag proteins. Collectively, our results underscore the ability of IL-27 to protect macrophages from HIV-1 infection by down-regulating SPTBN1, thus indicating that SPTBN1 is an important host target to reduce HIV-1 replication in one major element of the viral reservoir.
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Affiliation(s)
- Lue Dai
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Kristy B. Lidie
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Qian Chen
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Joseph W. Adelsberger
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Xin Zheng
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - DaWei Huang
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jun Yang
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Richard A. Lempicki
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Tauseef Rehman
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Robin L. Dewar
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Yanmei Wang
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Ronald L. Hornung
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Kelsey A. Canizales
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Stephen J. Lockett
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - H. Clifford Lane
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Tomozumi Imamichi
- Applied and Developmental Directorate and Advanced Technology Program Directorate, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
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96
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Joshi P, Sloan B, Torbett BE, Stoddart CA. Heat shock protein 90AB1 and hyperthermia rescue infectivity of HIV with defective cores. Virology 2013; 436:162-72. [PMID: 23200770 PMCID: PMC3563299 DOI: 10.1016/j.virol.2012.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/25/2012] [Accepted: 11/10/2012] [Indexed: 12/15/2022]
Abstract
We previously showed that reduced infectivity of HIV with incompletely processed capsid-spacer protein 1 (CA-SP1) is rescued by cellular activation or increased expression of HSP90AB1, a member of the cytosolic heat shock protein 90 family. Here we show that HSP90AB1 is present in HIV virions and that HSP90AB1, but not nonfunctional mutated HSP90AB1(E42A+D88A), restores infectivity to HIV with mutations in CA that alter core stability. Further, the CA mutants were hypersensitive to pharmacological inhibition of HSP90AB1. In agreement with Roesch et al. (2012), we found that culturing HIV at 39.5°C enhanced viral infectivity up to 30-fold in human peripheral blood mononuclear cells (p=0.002) and rescued CA-mutant infectivity in nonactivated cells, concurrent with elevated expression of HSP90AB1 during hyperthermia. In sum, the transdominant effect of HSP90AB1 on CA-mutant HIV infectivity suggests a potential role for this class of cellular chaperones in HIV core stability and uncoating.
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Affiliation(s)
- Pheroze Joshi
- Division of Experimental Medicine, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Barbara Sloan
- Division of Experimental Medicine, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Bruce E. Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cheryl A. Stoddart
- Division of Experimental Medicine, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, San Francisco, CA 94110, USA
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97
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Li W, Wang X, Gao G. Expression of YB-1 enhances production of murine leukemia virus vectors by stabilizing genomic viral RNA. Protein Cell 2012; 3:943-9. [PMID: 23225179 DOI: 10.1007/s13238-012-2090-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 09/04/2012] [Indexed: 12/25/2022] Open
Abstract
Murine leukemia virus (MLV)-based retroviral vectors is widely used for gene transfer and basic research, and production of high-titer retroviral vectors is very important. Here we report that expression of the Y-box binding protein 1 (YB-1) enhanced the production of infectious MLV vectors. YB-1 specifically increased the stability of viral genomic RNA in virus-producing cells, and thus increasing viral RNA levels in both producer cells and virion particles. The viral element responsive to YB-1 was mapped to the repeat sequence (R region) in MLV genomic RNA. These results identified YB-1 as a MLV mRNA stabilizer, which can be used for improving production of MLV vectors.
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Affiliation(s)
- Wei Li
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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98
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Milev MP, Ravichandran M, Khan MF, Schriemer DC, Mouland AJ. Characterization of staufen1 ribonucleoproteins by mass spectrometry and biochemical analyses reveal the presence of diverse host proteins associated with human immunodeficiency virus type 1. Front Microbiol 2012; 3:367. [PMID: 23125841 PMCID: PMC3486646 DOI: 10.3389/fmicb.2012.00367] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/27/2012] [Indexed: 12/02/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) unspliced, 9 kb genomic RNA (vRNA) is exported from the nucleus for the synthesis of viral structural proteins and enzymes (Gag and Gag/Pol) and is then transported to sites of virus assembly where it is packaged into progeny virions. vRNA co-exists in the cytoplasm in the context of the HIV-1 ribonucleoprotein (RNP) that is currently defined by the presence of Gag and several host proteins including the double-stranded RNA-binding protein, Staufen1. In this study we isolated Staufen1 RNP complexes derived from HIV-1-expressing cells using tandem affinity purification and have identified multiple host protein components by mass spectrometry. Four viral proteins, including Gag, Gag/Pol, Env and Nef as well as >200 host proteins were identified in these RNPs. Moreover, HIV-1 induces both qualitative and quantitative differences in host protein content in these RNPs. 22% of Staufen1-associated factors are virion-associated suggesting that the RNP could be a vehicle to achieve this. In addition, we provide evidence on how HIV-1 modulates the composition of cytoplasmic Staufen1 RNPs. Biochemical fractionation by density gradient analyses revealed new facets on the assembly of Staufen1 RNPs. The assembly of dense Staufen1 RNPs that contain Gag and several host proteins were found to be entirely RNA-dependent but their assembly appeared to be independent of Gag expression. Gag-containing complexes fractionated into a lighter and another, more dense pool. Lastly, Staufen1 depletion studies demonstrated that the previously characterized Staufen1 HIV-1-dependent RNPs are most likely aggregates of smaller RNPs that accumulate at juxtanuclear domains. The molecular characterization of Staufen1 HIV-1 RNPs will offer important information on virus-host cell interactions and on the elucidation of the function of these RNPs for the transport of Gag and the fate of the unspliced vRNA in HIV-1-producing cells.
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Affiliation(s)
- Miroslav P Milev
- HIV-1 Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital Montréal, QC, Canada ; Division of Experimental Medicine, Department of Medicine, McGill University Montreal, QC, Canada
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99
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Wight DJ, Boucherit VC, Nader M, Allen DJ, Taylor IA, Bishop KN. The gammaretroviral p12 protein has multiple domains that function during the early stages of replication. Retrovirology 2012; 9:83. [PMID: 23035841 PMCID: PMC3492146 DOI: 10.1186/1742-4690-9-83] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 09/19/2012] [Indexed: 01/07/2023] Open
Abstract
Background The Moloney murine leukaemia virus (Mo-MLV) gag gene encodes three main structural proteins, matrix, capsid and nucleocapsid and a protein called p12. In addition to its role during the late stages of infection, p12 has an essential, but undefined, function during early post-entry events. As these stages of retroviral infection remain poorly understood, we set out to investigate the function of p12. Results Examination of the infectivity of Mo-MLV virus-like particles containing a mixture of wild type and mutant p12 revealed that the N- and C-terminal regions of p12 are sequentially acting domains, both required for p12 function, and that the N-terminal activity precedes the C-terminal activity in the viral life cycle. By creating a panel of p12 mutants in other gammaretroviruses, we showed that these domains are conserved in this retroviral genus. We also undertook a detailed mutational analysis of each domain, identifying residues essential for function. These data show that different regions of the N-terminal domain are necessary for infectivity in different gammaretroviruses, in stark contrast to the C-terminal domain where the same region is essential for all viruses. Moreover, chimeras between the p12 proteins of Mo-MLV and gibbon ape leukaemia virus revealed that the C-terminal domains are interchangeable whereas the N-terminal domains are not. Finally, we identified potential functions for each domain. We observed that particles with defects in the N-terminus of p12 were unable to abrogate restriction factors, implying that their cores were impaired. We further showed that defects in the C-terminal domain of p12 could be overcome by introducing a chromatin binding motif into the protein. Conclusions Based on these data, we propose a model for p12 function where the N-terminus of p12 interacts with, and stabilizes, the viral core, allowing the C-terminus of p12 to tether the preintegration complex to host chromatin during mitosis, facilitating integration.
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Affiliation(s)
- Darren J Wight
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Pichlmair A, Kandasamy K, Alvisi G, Mulhern O, Sacco R, Habjan M, Binder M, Stefanovic A, Eberle CA, Goncalves A, Bürckstümmer T, Müller AC, Fauster A, Holze C, Lindsten K, Goodbourn S, Kochs G, Weber F, Bartenschlager R, Bowie AG, Bennett KL, Colinge J, Superti-Furga G. Viral immune modulators perturb the human molecular network by common and unique strategies. Nature 2012; 487:486-90. [PMID: 22810585 DOI: 10.1038/nature11289] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 06/07/2012] [Indexed: 12/24/2022]
Abstract
Viruses must enter host cells to replicate, assemble and propagate. Because of the restricted size of their genomes, viruses have had to evolve efficient ways of exploiting host cell processes to promote their own life cycles and also to escape host immune defence mechanisms. Many viral open reading frames (viORFs) with immune-modulating functions essential for productive viral growth have been identified across a range of viral classes. However, there has been no comprehensive study to identify the host factors with which these viORFs interact for a global perspective of viral perturbation strategies. Here we show that different viral perturbation patterns of the host molecular defence network can be deduced from a mass-spectrometry-based host-factor survey in a defined human cellular system by using 70 innate immune-modulating viORFs from 30 viral species. The 579 host proteins targeted by the viORFs mapped to an unexpectedly large number of signalling pathways and cellular processes, suggesting yet unknown mechanisms of antiviral immunity. We further experimentally verified the targets heterogeneous nuclear ribonucleoprotein U, phosphatidylinositol-3-OH kinase, the WNK (with-no-lysine) kinase family and USP19 (ubiquitin-specific peptidase 19) as vulnerable nodes in the host cellular defence system. Evaluation of the impact of viral immune modulators on the host molecular network revealed perturbation strategies used by individual viruses and by viral classes. Our data are also valuable for the design of broad and specific antiviral therapies.
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Affiliation(s)
- Andreas Pichlmair
- CeMMResearch Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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